Protists have fascinated microbiologists since their discovery nearly 350 years ago. These single-celled, eukaryotic species span an incredible range of sizes, forms, and functions and, despite their generally diminutive size, constitute much of the genetic diversity within the domain Eukarya. Protists in marine ecosystems play fundamental ecological roles as primary producers, consumers, decomposers, and trophic links in aquatic food webs. Much of our knowledge regarding the diversity and ecological activities of these species has been obtained during the past half century, and only within the past few decades have hypotheses depicting the evolutionary relationships among the major clades of protists attained some degree of consensus. This recent progress is attributable to the development of genetic approaches, which have revealed an unexpectedly large diversity of protists, including cryptic species and previously undescribed clades of protists. New genetic tools now exist for identifying protistan species of interest and for reexamining long-standing debates regarding the biogeography of protists. Studies of protistan diversity provide insight regarding how species richness and community composition contribute to ecosystem function. These activities support the development of predictive models that describe how microbial communities will respond to natural or anthropogenically mediated changes in environmental conditions.
DNA sequence information has increasingly been used in ecological research on microbial eukaryotes. Sequence-based approaches have included studies of the total diversity of selected ecosystems, studies of the autecology of ecologically relevant species, and identification and enumeration of species of interest for human health. It is still uncommon, however, to delineate protistan species based on their genetic signatures. The reluctance to assign species-level designations based on DNA sequences is in part a consequence of the limited amount of sequence information presently available for many free-living microbial eukaryotes and in part a consequence of the problematic nature of and debate surrounding the microbial species concept. Despite the difficulties inherent in assigning species names to DNA sequences, there is a growing need to attach meaning to the burgeoning amount of sequence information entering the literature, and there is a growing desire to apply this information in ecological studies. We describe a computer-based tool that assigns DNA sequences from environmental databases to operational taxonomic units at approximately species-level distinctions. This approach provides a practical method for ecological studies of microbial eukaryotes (primarily protists) by enabling semiautomated analysis of large numbers of samples spanning great taxonomic breadth. Derivation of the algorithm was based on an analysis of complete small-subunit (18S) rRNA gene sequences and partial gene sequences obtained from the GenBank database for morphologically described protistan species. The program was tested using environmental 18S rRNA data sets for two oceanic ecosystems. A total of 388 operational taxonomic units were observed for 2,207 sequences obtained from samples collected in the western North Atlantic and eastern North Pacific oceans.Ecological studies of aquatic microbial eukaryotes require identification and enumeration of organisms with extremely wide taxonomic diversity. The assemblages are typically dominated by phototrophic and heterotrophic protists (microalgae and protozoans), but microscopic metazoans belonging to a variety of animal phyla can also contribute significantly. Identification of protists in environmental samples is particularly difficult because most species have been defined morphologically (41, 84). Protistan identification involves a wide variety of procedures for collection, preservation, specimen preparation, and examination (34, 84), as well as many different types of taxonomic expertise. Very few studies have attempted to identify and enumerate all protistan taxa because of these complexities, which makes it difficult to evaluate ecological studies of protistan diversity, community structure, and biogeochemical function.The growing database of DNA sequence information for a wide spectrum of microbial eukaryotes offers the possibility for greatly improving the existing tools for studying the phylogeny and ecology of these organisms. Much of the initial impetus for the acquisition ...
The structure and genetic diversity of marine protistan assemblages were investigated in the upper 500 m of the water column at a Pacific Ocean time-series station off the coast of Southern California. Deoxyribonucleic acid sequence-based microbial eukaryote diversity was examined in January, April, July, and October of 2001 at four depths (5 m, chlorophyll maximum [CM], 150 m, and 500 m). A total of 2956 partial 18S ribosomal ribonucleic acid gene sequences yielded representatives from most of the major eukaryotic lineages. Notable among the taxonomic groups were recently described lineages of stramenopiles, alveolates, and euglenozoa. A large number of polycystine and acantharean sequences were observed at depth. Pairwise sequence analysis was performed to establish operational taxonomic units (OTUs) that were then used to estimate the unsampled protistan diversity by parametric and nonparametric techniques. A total of 2246 protistan sequences grouped into 377 distinct OTUs, with remaining sequences attributed to metazoa. Protistan richness estimates ranged from , 600 to 1500 OTUs when all depths and seasons were combined into a single data set. Seasonal and depth-related trends in the observed protistan diversity were apparent from comparisons of univariate and multivariate analyses. Cluster analysis combined with nonmetric multidimensional scaling and analysis of similarity testing identified distinct protistan assemblages at the shallowest depths (5 m and CM) for each season, which were significantly different (p , 0.03) from assemblages at the two deepest depths (150 and 500 m) where seasonal changes in the protistan assemblage were not apparent.
Coastal acidification in southeastern U.S. estuaries and coastal waters is influenced by biological activity, runoff from the land, and increasing carbon dioxide in the atmosphere. Acidification can negatively impact coastal resources such as shellfish, finfish, and coral reefs, and the communities that rely on them. Organismal responses for species located in the U.S. Southeast document large negative impacts of acidification, especially in larval stages. For example, the toxicity of pesticides increases under acidified conditions and the combination of acidification and low oxygen has profoundly negative influences on genes regulating oxygen consumption. In corals, the rate of calcification decreases with acidification and processes such as wound recovery, reproduction, and recruitment are negatively impacted. Minimizing the changes in global ocean chemistry will ultimately depend on the reduction of carbon dioxide emissions, but adaptation to these changes and mitigation of the local stressors that exacerbate global acidification can be addressed locally. The evolution of our knowledge of acidification, from basic understanding of the problem to the emergence of applied research and monitoring, has been facilitated by the development of regional Coastal Acidification Networks (CANs) across the United States. This synthesis is a product of the Southeast Coastal and Ocean Acidification Network (SOCAN). SOCAN was established to better understand acidification in the coastal waters of the U.S. Southeast and to foster communication among scientists, resource managers, businesses, and governments
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